Hi guys,

Strangely enough I do not get this error from here in Seattle (on openSUSE).

The tarballs for all the annotation packages can always be found on our
web site if biocLite should ever fail you (or if you just want to see
what is in the source code):

http://www.bioconductor.org/packages/release/data/annotation/


I also see that Harry is not using the most recent version of
AnnotationDbi for your version of R, so you might want to try and update
that as well.

biocLite("AnnotationDbi")


Also, since I can't reproduce the behavior that you guys are
experiencing, could you please let us know whatever you can about it? 


  Marc



On 09/21/2010 02:08 PM, James W. MacDonald wrote:
> Hi Harry,
>
> I get the same error you see, when I try to install on Linux. Weirdly
> enough, if I install from source on my Windows box I don't have any
> problems.
>
> And even weirder, I can install the source package on Linux if I use
> my local copy (I make the cdf packages for BioC, so I have the
> packages that I uploaded in April still sitting around).
>
> I would assume some corruption, if the package didn't install on
> Windows, but it does.
>
> Well, anyway, attached is the package that will install for me. See if
> it works for you.
>
> Best,
>
> Jim
>
>
>
> On 9/21/2010 3:55 PM, Harry Mangalam wrote:
>> Hi Jim,
>>
>> Thanks for the rapid reply, info and pointers.
>>
>> I tried to take your advice and on a larger machine (due to malloc
>> errors on the 1st - new sessionInfo() below) I can get a bit further
>> but still can't convince arrayQualityMetrics() to take or recognize
>> the appropriate cdf env.
>>
>>
>> While I include the entire session below, the main problem seems to be
>> that R will not conclude the installation of the CDF you referenced:
>>
>> biocLite("mogene10stv1cdf")
>>
>> either referenced separately or as part of the arrayQualityMetrics()
>> dependency.  It gave the identical results on the machine I used
>> before (w/ R 2.11.1) and on the larger 64b machine (w/ R 2.11.0).
>>
>> The entire session follows.
>> (From a clean start on the machine whose sessionInfo() is included at
>> beginning and end of the session.)
>>
>> $ module load R/2.11.0 # we use modules to keep things separate
>> $ R
>>> sessionInfo()
>> R version 2.11.0 (2010-04-22)
>> x86_64-unknown-linux-gnu
>>
>> locale:
>>   [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>>   [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>>   [5] LC_MONETARY=C              LC_MESSAGES=en_US.UTF-8
>>   [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
>>   [9] LC_ADDRESS=C               LC_TELEPHONE=C
>> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>>
>> attached base packages:
>> [1] graphics  grDevices datasets  stats     utils     methods   base
>>
>> other attached packages:
>> [1] Rmpi_0.5-8
>>
>>> library(affy)
>>> # deleted all 'std' output, including only errors or warnings.
>>
>> #create an affybatch object  from the cel files.
>>> ab<- ReadAffy(widget=TRUE)  # select all 8 wt cels (sal vs coc)
>>
>>> library("arrayQualityMetrics")
>> # and run the code on all the wt cels
>>> arrayQualityMetrics(expressionset = ab,outdir = "wt_sal_v_coc",force
>> = TRUE,do.logtransform = TRUE)
>> Loading required package: affyPLM
>> Loading required package: gcrma
>> Loading required package: preprocessCore
>>
>> Attaching package: 'affyPLM'
>>
>> The following object(s) are masked from 'package:stats':
>>
>>      resid, residuals, weights
>>
>>> arrayQualityMetrics(expressionset = ab,outdir = "wt_sal_v_coc",force
>> = TRUE,do.logtransform = TRUE)
>> The report will be written in directory 'wt_sal_v_coc'.
>> trying URL
>> 'http://bioconductor.org/packages/2.6/data/annotation/src/contrib/mogene10stv1cdf_2.6.2.tar.gz'
>>
>> Content type 'application/x-gzip' length 3126174 bytes (3.0 Mb)
>> opened URL
>> ==================================================
>> downloaded 3.0 Mb
>>
>> * installing *source* package ‘mogene10stv1cdf’ ...
>> ** R
>> ** data
>> ** preparing package for lazy loading
>> ** help
>> *** installing help indices
>> ** building package indices ...
>> ** testing if installed package can be loaded
>> Error in get(name, envir = asNamespace(pkg), inherits = FALSE) :
>>    object 'annoStartupMessages' not found
>> ERROR: loading failed
>> * removing ‘/apps/R/2.11.0/lib64/R/library/mogene10stv1cdf’
>>
>> The downloaded packages are in
>>          ‘/tmp/Rtmpq2sQrq/downloaded_packages’
>> Updating HTML index of packages in '.Library'
>> Error in getCdfInfo(object) :
>>    Could not obtain CDF environment, problems encountered:
>> Specified environment does not contain MoGene-1_0-st-v1
>> Library - package mogene10stv1cdf not installed
>> Library - package mogene10stv1cdf not installed
>> In addition: Warning message:
>> In install.packages(cdfname, lib = lib, repos =
>> Biobase:::biocReposList(),  :
>>    installation of package 'mogene10stv1cdf' had non-zero exit status
>>
>> <<the above stanza repeated 2 more times, downloading and then failing
>> to install the same pkg>>
>>
>> Is this a problem with matching case and intervening characters?
>> (mogene10stv1 vs MoGene-1_0-st-v1) or something more fundamental.
>>
>> I tried this as a user and as root, to see if it was a permissions
>> problem.  The results were identical.
>>
>> I also tried the installation of the CDF that came with the cel files.
>> (MoGene-1_0-st-v1.r3.cdf), but while this apparently went to
>> completion (as previously noted), it did not change anything.
>>
>> # at end of session, here is the sessionInfo()
>>> sessionInfo()
>> R version 2.11.0 (2010-04-22)
>> x86_64-unknown-linux-gnu
>>
>> locale:
>>   [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>>   [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>>   [5] LC_MONETARY=C              LC_MESSAGES=en_US.UTF-8
>>   [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
>>   [9] LC_ADDRESS=C               LC_TELEPHONE=C
>> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>>
>> attached base packages:
>> [1] tools     tcltk     graphics  grDevices datasets  stats     utils
>> [8] methods   base
>>
>> other attached packages:
>>   [1] arrayQualityMetrics_2.6.0 affyPLM_1.24.1
>>   [3] preprocessCore_1.10.0     gcrma_2.20.0
>>   [5] tkWidgets_1.26.0          DynDoc_1.26.0
>>   [7] widgetTools_1.26.0        affy_1.26.1
>>   [9] Biobase_2.8.0             Rmpi_0.5-8
>>
>> loaded via a namespace (and not attached):
>>   [1] affyio_1.16.0        annotate_1.26.1      AnnotationDbi_1.10.0
>>   [4] beadarray_1.16.0     Biostrings_2.16.9    DBI_0.2-5
>>   [7] genefilter_1.30.0    grid_2.11.0          hwriter_1.2
>> [10] IRanges_1.6.17       lattice_0.18-5       latticeExtra_0.6-11
>> [13] limma_3.4.5          marray_1.26.0        RColorBrewer_1.0-2
>> [16] RSQLite_0.8-4        simpleaffy_2.24.0    splines_2.11.0
>> [19] stats4_2.11.0        survival_2.35-8      vsn_3.16.0
>> [22] xtable_1.5-6
>>
>> Thanks for your consideration.
>>
>> harry
>>
>>
>> On Tuesday 21 September 2010 06:49:38 James W. MacDonald wrote:
>>> Hi Harry,
>>>
>>> On 9/20/2010 6:20 PM, Harry Mangalam wrote:
>>>> Hi BioC
>>>>
>>>> (sessionInfo() at bottom)
>>>>
>>>> I'm trying to help a group here do some QC on their affy datasets
>>>> derived from the mogene10stv1 array set.  This array is not in
>>>> mainstream BioC support but I've created and installed the CDF
>>>
>>>> environment for that array:
>>> This is not correct.
>>>
>>> biocLite("mogene10stv1cdf")
>>>
>>> Will get you the package you create below.
>>>
>>>>>    make.cdf.package("MoGene-1_0-st-v1.r3.cdf", species =
>>>>>    "Mus_mus")
>>>>
>>>> (completes, and I've installed the generated CDF env)
>>>>
>>>> but when I try to run  QCReport on this dataset (even explicitly
>>>
>>>> specifying the mogene10stv1 CDF env), I get the errors:
>>> In future, please mention the package you are using. I happen to
>>> know that QCReport() is part of the affyQCReport package, but by
>>> neglecting to include this bit of information you seriously
>>> degrade your chances of an answer.
>>>
>>> Now on to the answer. ;-D
>>>
>>> You are not going to be very satisfied with affyQCReport for this
>>> chip, as it uses the simpleaffy package for much of the quality
>>> control output, a good portion of which is based on MAS5 calls.
>>> Since the MoGene chip is a PM-only chip, you won't be able to
>>> compute MAS5 calls, as they rely on the matching MM probes, which
>>> don't exist. Hence the NA values below.
>>>
>>> I believe you will be better off using the arrayQualityMetrics
>>> package, which is more general.
>>>
>>> Best,
>>>
>>> Jim
>>>
>>>>> QCReport(ReadAffy(widget=TRUE,cdfname="mogene10stv1cdf"))
>>>>
>>>> #   or
>>>>
>>>>> QCReport(ReadAffy(widget=TRUE,cdfname="mogene10stv1"))
>>>>
>>>> #   (get same error)
>>>>
>>>> Error: NAs in foreign function call (arg 1)
>>>> In addition: Warning messages:
>>>>
>>>> 1: In data.row.names(row.names, rowsi, i) :
>>>>     some row.names duplicated:
>>>> 4,8,9,13,14,15,16,24,25,26,27,28,29,30,31,36,37,38,39,47,48,49,50
>>>> ,51,52,53,54,58,59,60,64,65,66,83,84,85,86,87,88,89,90,91,92,93,9
>>>> 4,95,96,97,98,99,102,103,104,108,109,110,111,114,119,120,121,122,
>>>> 127,134,136,137,138,139,141,142,147,148,149,152,153,156,157,158,1
>>>> 59,162,163,164,165,166,167,168,169,170,171,173,175,176,179,180,18
>>>> 3,184,185,186,191,192,195,197,198,199,200,202,206,207,210,219,220
>>>> ,227,228,229,230,233,234,235,240,241,243,245,246,248,249,250,251,
>>>> 252,253,257,259,260,266,271,272,276,277,280,281,284,286,287,289,2
>>>> 90,291,292,296,297,298,302,304,305,306,310,311,312,313,317,318,31
>>>> 9,321,322,324,334,337,338,339,340,341,345,346,350,351,356,359,362
>>>> ,364,366,367,370,371,373,376,378,382,383,384,385,386,387,388,389,
>>>> 391,394,395,397,398,399,400,402,403,405,406,407,409,410,411,415,4
>>>> 16,418,419,425,431,432,433,434,435,440,441,443,445,447,449,450,45
>>>> 2,454,455,456,461,464,466,470,472,473,481,487,488,491,492,493,494
>>>> ,495,496,497,498,499,501,502,504,506,507,509,511,513,515,516,51
>>>> [... truncated]
>>>>
>>>> 2: In qc.affy(unnormalised, ...) :
>>>>     CDF Environment name ' hgu95av2cdf ' does not match cdfname '
>>>>
>>>> mogene10stv1cdf '
>>>>
>>>> Error in plot(qc(object)) :
>>>>     error in evaluating the argument 'x' in selecting a method for
>>>>
>>>> function 'plot'
>>>>
>>>>
>>>> This: /Error: NAs in foreign function call (arg 1)/
>>>>
>>>>    seems to imply that:
>>>> - there's an error in the '(arg 1)'  but which (arg 1)?
>>>>
>>>>     If this refers to the arg
>>>>
>>>> /ReadAffy(widget=TRUE,cdfname="mogene10stv1cdf")/
>>>>
>>>>     then that part of the command seems to complete fine and
>>>>     returns an
>>>>
>>>> AffyBatch object as it should
>>>>
>>>>> str(rawdata)
>>>>
>>>> Formal class 'AffyBatch' [package "affy"] with 10 slots
>>>>
>>>>     ..@ cdfName          : chr "mogene10stv1cdf"
>>>>     ..@ nrow             : int 1050
>>>>     ..@ ncol             : int 1050
>>>>
>>>> /etc/
>>>>
>>>>
>>>> - or I have NAs in the data, but doesn't point to where or
>>>> whether I should address them.
>>>> If this is the critical error, I'm guessing I have to choose a
>>>> transform that removes or floor-shifts the NAs into a
>>>> computational form?
>>>>
>>>> - the Warnings:
>>>>
>>>> 1: In data.row.names(row.names, rowsi, i) :
>>>>     some row.names duplicated:
>>>>     4,8,9,13,14,15,16,24,25,26,27,28,29,<almost every
>>>>     intervening # omitted>
>>>>     ,513,515,516,51 [... truncated]
>>>>
>>>> Would this be related to warning 2 below?
>>>>
>>>> 2: In qc.affy(unnormalised, ...) :
>>>>     CDF Environment name ' hgu95av2cdf ' does not match cdfname '
>>>>
>>>> mogene10stv1cdf '
>>>>
>>>> but if so, what is the proper way to tell QCReport that I'm using
>>>> a non-default CDF?
>>>> the help section for QCReport doesn't describe any params for
>>>> telling it that the CDF env is not 'hgu95av2cdf' and I've tried
>>>> including that info in the ReadAffy() fn as noted:
>>>>
>>>> ie:
>>>>> QCReport(ReadAffy(widget=TRUE,cdfname="mogene10stv1"))
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> sessionInfo()
>>>>
>>>> R version 2.11.1 (2010-05-31)
>>>> i486-pc-linux-gnu
>>>>
>>>> locale:
>>>>    [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>>>>    [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>>>>    [5] LC_MONETARY=C              LC_MESSAGES=en_US.UTF-8
>>>>    [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
>>>>    [9] LC_ADDRESS=C               LC_TELEPHONE=C
>>>>
>>>> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>>>>
>>>> attached base packages:
>>>> [1] tools     tcltk     stats     graphics  grDevices utils
>>>> datasets
>>>> [8] methods   base
>>>>
>>>> other attached packages:
>>>>    [1] makecdfenv_1.26.0     tkWidgets_1.26.0      DynDoc_1.26.0
>>>>    [4] widgetTools_1.26.0    hgu95av2cdf_2.6.0
>>>>    affydata_1.11.10 [7] affyQCReport_1.26.0   lattice_0.19-11
>>>>      RColorBrewer_1.0-2
>>>>
>>>> [10] affyPLM_1.24.1        preprocessCore_1.10.0 xtable_1.5-6
>>>> [13] simpleaffy_2.24.0     gcrma_2.20.0
>>>> genefilter_1.30.0 [16] mogene10stv1cdf_2.6.2 affy_1.26.1
>>>>    Biobase_2.8.0
>>>>
>>>> loaded via a namespace (and not attached):
>>>>    [1] affyio_1.16.0        annotate_1.26.1
>>>>    AnnotationDbi_1.10.2 [4] Biostrings_2.16.9    DBI_0.2-5
>>>>        grid_2.11.1 [7] IRanges_1.6.17       RSQLite_0.9-2
>>>>    splines_2.11.1
>>>>
>>>> [10] survival_2.35-8
>>>>
>>>>
>>>> Thanks for your consideration.
>>
>
>
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